Per https://github.com/caskroom/homebrew-cask/issues/8052#issuecomment-69518811, looks like paths to homebrew's staging directories were added to 2.6.
Strangely, on a fresh install, they aren't shown--until you hit the "Reset" button by Search Scope, and then they're inserted.
The following screenshots are with no sync directory, and starting Alfred immediately after deleting ~/Library/Application Support/Alfred 2:
Pre-reset:
(http://i.imgur.com/mvDNTGy.png)
Post-reset:
(http://i.imgur.com/YhFH4Ec.png)
Note the additional /usr/local/Cellar and /opt/homebrew-cask/Caskroom paths after resetting. My best guess is that a "default" prefs file is written that doesn't include the late adds of the paths.
Distilled Bug Report
1. Install Alfred 2 (I used brew cask to install, but it shows on any "new" prefs file).
2. Ensure that Alfred 2 is not running
3. Ensure that no ~/Library/Application Support/Alfred 2 directory exists, or that default exists
4. Start Alfred 2
5. Navigate to Features
Expected: homebrew-related paths in search scope
Actual: no homebrew-related paths
6. Press "Reset"
Expected=Actual: homebrew-related paths appear
7. Close Alfred 2 completely
8. Delete ~/Library/Application Support/Alfred 2
9. Re-open Alfred 2
10. Note that behavior recurs, as in step 5 forward, and scope again omits homebrew.